2010-10-18    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: MAXOSX, look for gpl3.txt in the ../doc directory.

	* Makefile (Makefile.libplugin): Removed -makefile qmake option.

	* VirtualLeaf.cpp (TIMESTEP): Removed getIterations().

	* mesh.h (Mesh): Removed {increment,get}Iterations().

	* canvas.cpp (TimeStepWrap): Replaced getIterations() with getTime().

2010-10-15    <guravage@caterpie.sen.cwi.nl>

	* mesh.h (Mesh): Added iterations. incrementIterations() and

	getIterations().

	* VirtualLeaf.cpp (Plot): Replaced local frame counter with

	mesh.incrementIterations().

	* canvas.cpp (TimeStepWrap): Replaced local counter with

	mesh.incrementIterations().

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Turned debug off to make all profiles must be

	consistant.

	* VirtualLeaf-install.nsi: Tweaked paths to coincide with UNIX

	distribution, i.e. VirtualLeaf.exe, its libraries, models, and the

	uninstaller all go in the bin directory. And leaves directory

	placed under data directory.

	* canvas.cpp (exportCellData): Added a check to inquire before

	overwritting an existing file.

2010-10-14    <merks@cwi.nl>

	* mesh.cpp: In response to referees' comments, added new parameter

	"yield_threshold" instead of fixed parameter '4' for yield

	threshold.

	* wallitem.cpp: when clicking a wall, both the wall type was

	cycled and the transporterdialog popped up. Corrected this - for

	wall type cycling, hold the Control button while left

	clicking. TransporterDialog only pops up for left click. Also made

	sure the wall is redrawn after changing the transporter values.

	* cell.cpp (DivideWalls): accomodated for rename of Circumference -> WallCircumference

	* hull.h: added an operator< to sort Points

	* hull.cpp: added an operator< to sort Points

	* cellbase.cpp (ExactCircumference): I added a new function

	ExactCircumference, yielding the circumference of the cell along

	its wall_elements

	* VirtualLeaf.cpp: adjust info_string to accomodate for new name

	of function CellBase::Circumference -> CellBase::WallCircumference

	* mesh.cpp: corrected Mesh::Compactness, the boundary coordinates

	need to be sorted in x,y order for the convex hull algorithm

	(thanks Margriet!). I updated CSVExportCellData so it exports the

	circumferences of hull and boundary_polygon.

2010-10-14    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeafpar.tmpl (export_fn_prefix): changed to 'cell.'

	* canvas.cpp (TimeStepWrap): Removed TimeStamp(). Cell data

	filename now incorporates iteration number.

	* canvas.h (MainBase): Removed TimeStamp().

2010-10-08    <guravage@caterpie.sen.cwi.nl>

	* pardialog.h:

	* pardialog.cpp:

	* parameter.h:

	* parameter.cpp: Regenerated to include export_interval and export_fn_prefix.

	* VirtualLeafpar.tmpl: Appended export_interval and export_fn_prefix.

	* canvas.h (MainBase): Declared polymorphic exportCellData() functions.

	* canvas.cpp:

	(TimeStamp): New private TimeStamp() function.

	(TimeStepWrap): Added invocation of exportCellData().

	(exportCellData): Created two polymorphic functions: one with a

	single QString argument, the other with no argument. The former is

	called from TimeStepWrap() while the latter is called from the

	"Export cell areas" item in the file menu.

2010-10-07    <guravage@caterpie.sen.cwi.nl>

	* canvas.cpp (exportCellData): Added a Q3FileDialog to inquire

	where to write the exportCellData.

2010-06-28    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf-install.nsi: Grab gpl3.txt from doc directory.

	* canvas.cpp (gpl): gpl3.txt can be either in an ancestor doc

	directory (Linux) or a decedent doc directory (Windows, via the

	binary installer).

	* VirtualLeaf-install.nsi: Add VirtualLeaf doc directory.

2010-06-25    <guravage@caterpie.sen.cwi.nl>

	* gpl3.txt: Moved gpl3.txt from doc to src directory.

	* VirtualLeaf.pro: Added -Wno-write-strings and -Wno-unused-parameter to QMAKE_CXXFLAGS.

	* libplugin.pro: Ditto.

	* parameter.cpp: Result of adding datadir changes to make_parameter_source.pl.

	* parameter.h: Ditto.

	* output.h: Declared new function (AppendHomeDirIfPathRelative).

	* output.cpp (AppendHomeDirIfPathRelative): Added new function.

	* canvas.cpp (gpl): Moving gpl3.txt from doc to src obviates the need to docDir.cd("../doc").

	* VirtualLeaf-install.nsi: Grab gpl3.txt from src directory.

	Add missing libiconv/bin, libxml2bin and libz/bin directories.

	Copy libiconv-2.dll, libxml2.dll and zlib1.dll from relative paths.

	* VirtualLeaf.pro: copy gpl3.txt as part of QMAKE_POST_LINK.

2010-06-24    <guravage@caterpie.sen.cwi.nl>

	* libplugin.pro: Use correct library path.

	* VirtualLeaf.pro: Ditto.

	* VirtualLeaf.cpp (DrawCell): Iterate over NChem to construct info_string.

2010-06-23    <guravage@caterpie.sen.cwi.nl>

	* simitembase.cpp: Removed NULL assignments to unused variables.

	* VirtualLeaf.cpp: Ditto.

	* apoplastitem.cpp: Ditto.

	* canvas.cpp: Ditto.

	* cell.cpp: Ditto.

	* cellbase.h: Ditto.

	* forwardeuler.cpp: Ditto.

	* mainbase.h: Ditto.

	* nodeitem.cpp: Ditto.

	* qcanvasarrow.h: Ditto.

	* simitembase.cpp: Ditto.

	* Makefile (clean): Add -f Makefile argument to each make invocation.

	* VirtualLeaf-install.nsi: New gpl license text.

	* VirtualLeaf.pro: Disabled console mode.

	* mesh.cpp (Clear): Added parentheses to qDebug statments.

	(TestIllegalWalls): Replaced qDebug().

	* canvas.cpp (mouseReleaseEvent): Replaced qDebug() with cerr since qDebug complains about *node_set.

	* wall.cpp (CorrectWall): Rplaced gDebug() with cerr in transform call and when printing *this.

2010-06-22    <guravage@caterpie.sen.cwi.nl>

	* Makefile (tutorials): Add tutorials target.

2010-06-21    <guravage@caterpie.sen.cwi.nl>

	* parameter.cpp: Added particular reassignment of datadir.

	* canvas.cpp (gpl): Added GPL3 License text. Display detail text only if the source text file exists.

2010-06-18    <guravage@caterpie.sen.cwi.nl>

	* canvas.cpp (gpl): Added gpl slot to display GPL license.

	* VirtualLeaf.pro: Changed default LIBXML2DIR, LIBICONVDIR and LIBZDIR to corresponding distribution lib directories.

	* libplugin.pro: Ditto.

	* Makefile (clean): add if stmt not to `touch` on windows.

2010-06-17    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed perl references.

	* libplugin.pro: Ditto.

2010-06-15    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed xmlwritecode.cpp from SOURCES list.

	* xmlwrite.cpp (XMLSave): Removed references to XMLWriteLeafSourceCode and XMLWriteReactionsCode.

	* xmlwrite.h (XMLIO): Ditto!

	* mesh.cpp (findNextBoundaryNode): Initialize Node *next_boundary_node = NULL;

	* xmlwrite.cpp (XMLReadSimtime): Removed unused variable cur

	(XMLReadWalls): viz_flux need not be declared twice; default value of 0.0.

	(XMLReadCells): Removed unused count variable.

	(XMLReadSimtime): Removed unused cur variable.

	(XMLRead): Removed unused v_str variable.

	* simitembase.cpp (userMove): Use assignment merely to obviate compilation warning.

	(SimItemBase) Ditto.

	* qcanvasarrow.h (QGraphicsLineItem): Use assignment merely to obviate compilation warning.

	* output.cpp (OpenWriteFile): Removed unused par variable.

	* nodeitem.cpp (paint): Use assignment merely to obviate compilation warning.

	* forwardeuler.cpp (odeint): Use assignment merely to obviate compilation warning.

	* cell.cpp (DivideOverGivenLine): Use assignment merely to obviate compilation warning.

	* canvas.cpp (FigureEditor): Use assignments merely to obviate compilation errors.

	(mousePressEvent): Removed unused item variable.

	* apoplastitem.cpp

	(ApoplastItem): Removed unused par variable.

	(OnClick): Use NULL assignment merely to obviate compilation warning.

	* mainbase.h (MainBase): Use assignment merely to obviate compilation warning.

	* cellbase.h (CellsStaticDatamembers): Use assignment merely to obviate compilation warning.

	* cell.cpp: Wrapped diagnostic output in QDEBUG blocks.

	* VirtualLeaf.cpp ditto.

	* canvas.cpp ditto.

	* cell.cpp ditto.

	* data_plot.cpp ditto.

	* forwardeuler.cpp ditto.

	* mesh.cpp ditto.

	* mesh.h

	* random.cpp ditto.

	* wall.cpp ditto.

	* wallbase.cpp ditto.

	* wallitem.cpp ditto.

2010-06-07    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Removed explicit perl invocation to regerenerate parameter files.

	* libplugin.pro: ditto.

2010-06-03    <guravage@caterpie.sen.cwi.nl>

	* pardialog.h: Added default versions of this automatically generated file.

	* pardialog.cpp: ditto.

	* parameter.h: ditto.

	* parameter.cpp: ditto.

	* VirtualLeaf.pro: delete/generate  parameter.{h,cpp}and pardialog.{h,cpp} only if perl is installed.

 	* libplugin.pro: dito.

	* Makefile: Added top-level Makefile

2010-05-10    <guravage@caterpie.sen.cwi.nl>

	* VirtualLeaf.pro: Added -fPIC option to QMAKE_CXXFLAGS.

# $Id$

# appends \ to the path if missing

# example: !insertmacro GetCleanDir "c:\blabla"

# Pop $0 => "c:\blabla\"

!macro GetCleanDir INPUTDIR

  ; ATTENTION: USE ON YOUR OWN RISK!

  ; Please report bugs here: http://stefan.bertels.org/

  !define Index_GetCleanDir 'GetCleanDir_Line${__LINE__}'

  Push $R0

  Push $R1

  StrCpy $R0 "${INPUTDIR}"

  StrCmp $R0 "" ${Index_GetCleanDir}-finish

  StrCpy $R1 "$R0" "" -1

  StrCmp "$R1" "\" ${Index_GetCleanDir}-finish

  StrCpy $R0 "$R0\"

${Index_GetCleanDir}-finish:

  Pop $R1

  Exch $R0

  !undef Index_GetCleanDir

!macroend

# similar to "RMDIR /r DIRECTORY", but does not remove DIRECTORY itself

# example: !insertmacro RemoveFilesAndSubDirs "$INSTDIR"

!macro RemoveFilesAndSubDirs DIRECTORY

  # ATTENTION: USE ON YOUR OWN RISK!

  # Please report bugs here: http://stefan.bertels.org/

  !define Index_RemoveFilesAndSubDirs 'RemoveFilesAndSubDirs_${__LINE__}'

  Push $R0

  Push $R1

  Push $R2

  !insertmacro GetCleanDir "${DIRECTORY}"

  Pop $R2

  FindFirst $R0 $R1 "$R2*.*"

${Index_RemoveFilesAndSubDirs}-loop:

  StrCmp $R1 "" ${Index_RemoveFilesAndSubDirs}-done

  StrCmp $R1 "." ${Index_RemoveFilesAndSubDirs}-next

  StrCmp $R1 ".." ${Index_RemoveFilesAndSubDirs}-next

  IfFileExists "$R2$R1\*.*" ${Index_RemoveFilesAndSubDirs}-directory

  ; file

  Delete "$R2$R1"

  goto ${Index_RemoveFilesAndSubDirs}-next

${Index_RemoveFilesAndSubDirs}-directory:

  ; directory

  RMDir /r "$R2$R1"

${Index_RemoveFilesAndSubDirs}-next:

  FindNext $R0 $R1

  Goto ${Index_RemoveFilesAndSubDirs}-loop

${Index_RemoveFilesAndSubDirs}-done:

  FindClose $R0

  Pop $R2

  Pop $R1

  Pop $R0

  !undef Index_RemoveFilesAndSubDirs

!macroend

!define PRODUCT_NAME "The Virtual Leaf"

!define PRODUCT_VERSION "1.0"

!define PRODUCT_PUBLISHER "Center for Mathematics and Computer Science (CWI)"

!define PRODUCT_WEB_SITE "www.cwi.nl"

!define EXECUTABLE "VirtualLeaf.exe"

!define PROGICON "leaficon.ico"

!define SETUP_BITMAP "leaficon.ico"

# MUI 1.67 compatible ------

!include "MUI.nsh"

!include "EnvVarUpdate.nsh"

# MUI Settings

!define MUI_ABORTWARNING

!define MUI_ICON "leaficon.ico"

!define MUI_UNICON "leaficon.ico"

# Welcome page

!insertmacro MUI_PAGE_WELCOME

# License page

!insertmacro MUI_PAGE_LICENSE "..\doc\gpl3.txt"

# Components page

!insertmacro MUI_PAGE_COMPONENTS

# Directory page

!insertmacro MUI_PAGE_DIRECTORY

# Instfiles page

!insertmacro MUI_PAGE_INSTFILES

# Finish page

!insertmacro MUI_PAGE_FINISH

# Uninstaller pages

!insertmacro MUI_UNPAGE_CONFIRM

!insertmacro MUI_UNPAGE_INSTFILES

!insertmacro MUI_UNPAGE_FINISH

# Language files

!insertmacro MUI_LANGUAGE "English"

# MUI end ------

# set the name of the installer

outfile "VirtualLeaf-install.exe"

Name "${PRODUCT_NAME} ${PRODUCT_VERSION}"

ShowInstDetails show

ShowUnInstDetails show

# define the directory to install to

installDir C:\VirtualLeaf

# Request application privileges

RequestExecutionLevel user

section "Virtual Leaf executable"

  #sectionIn RO

  # define the output path for the Virtual Leaf executable

  setOutPath $INSTDIR\bin

  file ..\bin\VirtualLeaf.exe

  # Required DLLs

  setOutPath $INSTDIR\bin

  file ..\lib\libiconv\bin\libiconv-2.dll

  file ..\lib\libxml2\lib\libxml2.dll

  file ..\lib\libz\bin\zlib1.dll

  # Is the pegging of these DLLs to a specific QT version a problem?

  file C:\Qt\2010.02.1\mingw\bin\mingwm10.dll

  file C:\Qt\2010.02.1\mingw\bin\libgcc_s_dw2-1.dll

  file C:\Qt\2010.02.1\qt\bin\Qt3Support4.dll

  file C:\Qt\2010.02.1\qt\bin\QtCore4.dll

  file C:\Qt\2010.02.1\qt\bin\QtGui4.dll

  file C:\Qt\2010.02.1\qt\bin\QtNetwork4.dll

  file C:\Qt\2010.02.1\qt\bin\QtSql4.dll

  file C:\Qt\2010.02.1\qt\bin\QtXml4.dll

  # Prepend the Virtual Leaf bin directory to the installers PATH

  ${EnvVarUpdate} $0 "PATH" "P" "HKCU" "$INSTDIR\bin"  

sectionEnd

section "Virtual Leaf plugins"

  # define the output path for the Virtual Leaf models

  setOutPath $INSTDIR\bin\models

  file ..\bin\models\*

sectionEnd

section "Virtual Leaf data"

  # define the output path for the Virtual Leaf models

  setOutPath $INSTDIR\data\leaves

  file ..\data\leaves\*

sectionEnd

section "Virtual Leaf docs"

  # define the output path for the Virtual Leaf documentation

  setOutPath $INSTDIR\doc

  file ..\doc\*

sectionEnd

# create a section to define what the uninstaller does.

# the section will always be named "Uninstall"

section "Uninstall"

  # Always delete uninstaller first

  delete $INSTDIR\uninstaller.exe

  # Now delete installed file

  !insertmacro RemoveFilesAndSubDirs "$INSTDIR"

  # Last but not least - delete the path  

  ${un.EnvVarUpdate} $0 "PATH" "R" "HKCU" "$INSTDIR\bin"

sectionEnd

# finis

/*

 *

 *  This file is part of the Virtual Leaf.

 *

 *  VirtualLeaf is free software: you can redistribute it and/or modify

 *  it under the terms of the GNU General Public License as published by

 *  the Free Software Foundation, either version 3 of the License, or

 *  (at your option) any later version.

 *

 *  VirtualLeaf is distributed in the hope that it will be useful,

 *  but WITHOUT ANY WARRANTY; without even the implied warranty of

 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 *  GNU General Public License for more details.

 *

 *  You should have received a copy of the GNU General Public License

 *  along with the Virtual Leaf.  If not, see <http://www.gnu.org/licenses/>.

 *

 *  Copyright 2010 Roeland Merks.

 *

 */

#include <libxml/xpath.h>

#include <libxml/xmlreader.h>

#include "mainbase.h"

#include "xmlwrite.h"

#include <sstream>

#include <string>

#include <QLocale>

static const std::string _module_id("$Id$");

xmlNode *MainBase::XMLViewportTree(QTransform &transform) const {

  QLocale standardlocale(QLocale::C);

  xmlNode *xmlviewport = xmlNewNode(NULL, BAD_CAST "viewport");

  {

    xmlNewProp(xmlviewport, BAD_CAST "m11", BAD_CAST standardlocale.toString(transform.m11()).toStdString().c_str() );

    xmlNewProp(xmlviewport, BAD_CAST "m12", BAD_CAST standardlocale.toString(transform.m12()).toStdString().c_str() );    

    xmlNewProp(xmlviewport, BAD_CAST "m21", BAD_CAST standardlocale.toString(transform.m21()).toStdString().c_str() );    

    xmlNewProp(xmlviewport, BAD_CAST "m22", BAD_CAST standardlocale.toString(transform.m22()).toStdString().c_str() );    

    xmlNewProp(xmlviewport, BAD_CAST "dx", BAD_CAST standardlocale.toString(transform.dx()).toStdString().c_str() );    

    xmlNewProp(xmlviewport, BAD_CAST "dy", BAD_CAST standardlocale.toString(transform.dy()).toStdString().c_str() );    

 }

  return xmlviewport;

}

xmlNode *MainBase::XMLSettingsTree(void) const {

  xmlNode *xmlsettings = xmlNewNode(NULL, BAD_CAST "settings");

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_centers");

    ostringstream text;

    text << bool_name(showcentersp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_nodes");

    ostringstream text;

    text << bool_name(showmeshp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_node_numbers");

    ostringstream text;

    text << bool_name(shownodenumbersp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_numbers");

    ostringstream text;

    text << bool_name(showcellnumbersp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_border_cells");

    ostringstream text;

    text << bool_name(showbordercellp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_axes");

    ostringstream text;

    text << bool_name(showcellsaxesp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_cell_strain");

    ostringstream text;

    text << bool_name(showcellstrainp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_fluxes");

    ostringstream text;

    text << bool_name(showfluxesp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_walls");

    ostringstream text;

    text << bool_name(showwallsp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

 /* {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_apoplasts");

    ostringstream text;

    text << bool_name(showapoplastsp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }*/

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "save_movie_frames");

    ostringstream text;

    text << bool_name(movieframesp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "show_only_leaf_boundary");

    ostringstream text;

    text << bool_name(showboundaryonlyp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "cell_growth");

    ostringstream text;

    text << bool_name(dynamicscellsp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  {

    xmlNode *xmloption = xmlNewChild(xmlsettings, NULL, BAD_CAST "setting", NULL);

    xmlNewProp(xmloption, BAD_CAST "name", BAD_CAST "hide_cells");

    ostringstream text;

    text << bool_name(hidecellsp);

    xmlNewProp(xmloption, BAD_CAST "val", BAD_CAST text.str().c_str());

  }

  return xmlsettings;

}

void MainBase::XMLReadViewport(xmlNode *settings) {

  if (settings == 0) {

    return;

  }

  qreal m11=25,m12=0,m21=0,m22=25,dx=0,dy=0;

  QLocale standardlocale(QLocale::C);

  xmlNode *cur = settings->xmlChildrenNode;

  while (cur!=NULL) {

    if (!xmlStrcmp(cur->name,(const xmlChar *)"viewport")) {

      bool ok;

      {

	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "m11");

	if (v_str==0) {

	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");

	}

	if (v_str != NULL) {

	  m11=standardlocale.toDouble((char *)v_str, &ok);

	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);

	  xmlFree(v_str);

	}

      }

      {

	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "m12");

	if (v_str==0) {

	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");

	}

	if (v_str != NULL) {

	  m12=standardlocale.toDouble((char *)v_str, &ok);

	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);

	  xmlFree(v_str);

	}

      }

      { 

	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "m21");

	if (v_str==0) {

	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");

	}

	if (v_str != NULL) {

	  m21=standardlocale.toDouble((char *)v_str, &ok);

	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);

	  xmlFree(v_str);

	}

      }

      {

	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "m22");

	if (v_str==0) {

	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");

	}

	if (v_str != NULL) {

	  m22=standardlocale.toDouble((char *)v_str, &ok);

	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);

	  xmlFree(v_str);

	}

      }

      {

	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "dx");

	if (v_str==0) {

	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");

	}

	if (v_str != NULL) {

	  dx=standardlocale.toDouble((char *)v_str, &ok);

	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);

	  xmlFree(v_str);

	}

      }

      {

	xmlChar *v_str = xmlGetProp(cur, BAD_CAST "dy");

	if (v_str==0) {

	  MyWarning::unique_warning("Error reading viewport in mainbase.cpp");

	}

	if (v_str != NULL) {

	  dy=standardlocale.toDouble((char *)v_str, &ok);

	  if (!ok) MyWarning::error("Could Not Convert \"%S\" To Double In XMLRead.",(char *)v_str);

	  xmlFree(v_str);

	}

      }

    }

    cur=cur->next;

  }

  viewport = QTransform(m11,m12,m21,m22,dx,dy);

}

void MainBase::XMLReadSettings(xmlNode *settings)

{

  // Many files have no settings section, so don't complain about it.

  // Defaults will be used instead.

  if (settings == 0) {

    return;

  }

  XMLReadViewport(settings);

  xmlNode *cur = settings->xmlChildrenNode;

  while (cur!=NULL) {

    if ((!xmlStrcmp(cur->name, (const xmlChar *)"setting"))){

      xmlChar *name = xmlGetProp(cur, BAD_CAST "name");

      xmlChar *val = xmlGetProp(cur, BAD_CAST "val");

      if (!xmlStrcmp(name, (const xmlChar *)"show_cell_centers")) {

	showcentersp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_nodes")) {

	showmeshp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_node_numbers")) {

	shownodenumbersp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_cell_numbers")) {

	showcellnumbersp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_border_cells")) {

	showbordercellp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_cell_axes")) {

	showcellsaxesp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_cell_strain")) {

	showcellstrainp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_fluxes")) {

	showfluxesp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_walls")) {

	showwallsp = strtobool( (const char *)val );

      }

     /* if (!xmlStrcmp(name, (const xmlChar *)"show_apoplasts")) {

	showapoplastsp = strtobool( (const char *)val );

      }*/

      if (!xmlStrcmp(name, (const xmlChar *)"save_movie_frames")) {

	movieframesp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"show_only_leaf_boundary")) {

	showboundaryonlyp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name, (const xmlChar *)"cell_growth")) {

	dynamicscellsp = strtobool( (const char *)val );

      }

      if (!xmlStrcmp(name,(const xmlChar *)"hide_cells")) {

	hidecellsp = strtobool( (const char *)val ); 

      }

      xmlFree(name);

      xmlFree(val);

    }

    cur=cur->next;

  }

}

void MainBase::Save(const char *fname, const char *format, int sizex, int sizey)

{

  Vector ll,ur;

  mesh.BoundingBox(ll, ur);

  if (QString(fname).isEmpty()) {

    MyWarning::warning("No output filename given. Saving nothing.\n");

    return;

  }

  ll*=Cell::Magnification(); ur*=Cell::Magnification();

  // give the leaf some space

  Vector border = ((ur-ll)/5.);

  if (!QString(format).contains("pdf", Qt::CaseInsensitive)) {

    QImage *image = new QImage(QSize(sizex, sizey), QImage::Format_RGB32);

    image->fill(QColor(Qt::white).rgb());

    QPainter *painter=new QPainter(image);

    canvas.render(painter);

      MyWarning::warning("Image not saved successfully. Is the disk full or the extension not recognized?");

    };

    delete painter;

    delete image;

  } else {

    QPrinter pdf(QPrinter::HighResolution);

    pdf.setOutputFileName(fname);

    pdf.setOutputFormat(QPrinter::PdfFormat);

    QPainter painter(&pdf);

    canvas.render(&painter, QRectF(), QRectF(-5000,-5000, 10000, 10000));

    cerr << "Rendering to printer\n";

  }

}

void MainBase::CutSAM()

{

  mesh.CutAwaySAM();

}

/* finis */